If it's really muddy and you suspect something is up with your adults, I'd hold off till it dries up a bit. If you can find some sandy soil for a dust bath from a different part of the yard for the chicks inside, that would be good for exposure to stuff in the soil. If wet and damp isn't your norm, and the coops are not draining well, a few weeks inside more won't hurt and would likely be better.
For something like cocci which loves to live in wet soil, it is everywhere, however, if it goes though a bird and reproduces, the numbers can exponentially increase in areas where immune adults are living. A young chick can eat enough plain oocysts in the soil to get sick, even if they cannot reproduce in the gut due to medicated feed. That is a reason why medicated feed doesn't stop chicks from getting cocci, as it doesn't do much other than keep them from reproducing in the bird.
If you get the chance, if you could add drainage to the bottom of the runs maybe that would help with the mud. A few inches of sand should be able to do the trick.
Hope I made some sense, brain is a bit fried today from work.
